As per Chrome store feedback. This makes more sense, I don't know why I did it the way it is currently done. Even if the scope is not in use, HTTPSB shouldn't delete a cookie which could be used by that scope in the future.

A cookie sitting on the computer causes no harm, it's their sending to a remote host which causes harm, and if a cookie is whitelisted in at least one scope, it's best to let it sit locally as it will be reused as per user's choice later. This cookie won't be sent to remote hosts outside the scope where it is whitelisted, that's the important part.